Researchers have sequenced the DNA of plague bacteria from the bodies of …

The bacteria behind the Black Death has a very unusual history. Its ancestor is an unassuming soil bacterium and the current strains of Yersinia pestis still infects thousands of people annually, but no longer cause the suite of horrifying symptoms associated with the medieval plagues. The radical differences between the two versions, in fact, led some to suggest that we have been blaming the wrong bacteria. Now, researchers have obtained DNA from some of London's plague victims and confirmed that Y. pestis appears to be to blame. But the sequences also suggest that the strains of bacteria we see today may be different from the ones that rampaged through Europe.

What transformed soil bacteria into a human pathogen? One key event seems to have been the fact that it picked up a plasmid, a short, circular piece of DNA that can be copied separately from the rest of the organism's DNA. In the case of Y. pestis, that plasmid contained three key genes: two that helped it kill off competing bacteria, and a third that helped it manipulate the human blood clotting system. So, when presented with the opportunity to obtain the DNA of plague victims, this is the DNA the authors decided to target.

The DNA came from 53 bones and 46 teeth from the East Smithfield, a mass burial site in London that dates to the first appearance of the Black Death in Europe, from 1347-1351. This is a key resource, since the different waves of plague that swept through Europe had somewhat different behavior, suggesting that Y. pestis was already adapting to its human hosts. To serve as controls, the authors obtained bones from a set of 10 human remains that predate the appearance of the plague.

To figure out the degree of contamination, each of the sets of bones were used to search for the DNA of human mitochondria, which should provide a degree of information about the levels of damage and contamination. Some of the samples contained no DNA, but a significant number did. Contamination levels were manageable, and the sequence had the sorts of changes that are typical for older, damaged DNA. With the samples looking good, the authors turned to sequencing the Y. pestis plasmid DNA.

As an added layer of precaution, they sent their samples to two different sequencing facilities, neither of which had previously handled Y. pestis DNA. It was relatively easy to pick up plasmid DNA from the tooth samples, which the authors explain as being derived from the pulp, which is rich in the blood vessels that the bacteria prefer to inhabit. The DNA they obtained also showed indications of the same changes seen in the human sequence, indicating it was also likely to be old and have suffered the same damage over time. With sufficient sequences (they got as many as 37,000 from a single sample), they were able to reconstruct the sequence of the plasmid.

For the most part, the sequence is similar to that found in modern strains of the bacteria. In contrast, some of the DNA they obtained from the bacteria's chromosome showed some distinct differences, none of which are present in modern strains. Nevertheless, the sequence was clearly still from Y. pestis.

The authors conclude that this provides a clear indication that a single type of bacteria has been responsible for the Black Death and several other plague outbreaks, and is still causing modern diseases. For some of the parties involved, this is a bit of an about-face, one that was handled with a degree of candor that's rare in scientific publications.

"Two of the authors (SW and JM) have previously argued that the epidemiology, virulence, and population dynamics of the Black Death were too different from those factors of modern yersinial plague to have been caused by Y. pestis," said the paper. "Given the growing body of evidence implicating this bacterium as responsible for the pandemic, we believe scientific debates should now shift to addressing the genetic basis of the epidemic’s unique characteristics."

This work is actually an important step in that shift, even though it's a negative result. The fact that this plasmid is not significantly different from the one carried by modern strains indicates the differences must reside elsewhere, and the initial sequencing of the bacteria's chromosome suggests that more work should be devoted to that. Chromosomes are quite a bit larger than a plasmid, though, and are likely to have many changes scattered across the DNA. Identifying which ones influence the bacteria's lethality could prove a serious challenge even if we can obtain the entire sequence.

Always pleasant to read a story which is essentially "Yup, this bacteria that took out between 1/5th and 1/3rd of the planet's human population is not only still around but has demonstrated an ability to ramp up its lethality by unknown means in response to unknown factors.".

Always pleasant to read a story which is essentially "Yup, this bacteria that took out between 1/5th and 1/3rd of the planet's human population is not only still around but has demonstrated an ability to ramp up its lethality by unknown means in response to unknown factors.".

How about that? Scientist makes new discovery, has to revise a past assumption. No problem, in fact a pleasant surprise.

So will we hear from all the religious nutjobs denouncing the findings and either saying the Black Plague didn't happen, or that The Devil™ is messing with the results and really it was wicked people who God™ smote?

I'm just thankful we are past the age of reason. Few are left who think prayer will heal the plague. If such an epidemic spreads again then we have the help of a better scientific process to curtail it's effect.

How about that? Scientist makes new discovery, has to revise a past assumption. No problem, in fact a pleasant surprise.

So will we hear from all the religious nutjobs denouncing the findings and either saying the Black Plague didn't happen, or that The Devil™ is messing with the results and really it was wicked people who God™ smote?

There has been discussion in the medical literature re: high mortality of hosts not being an evolutionary advantage for pathogens. If this is the case and v. pestis did pick up DNA that allowed it to exploit human hosts (to their extreme detriment) it's possible that evolutionary pressure decreased the mortality over time.

Are we entirely discounting the outbreak of 541 CE as bubonic plague? I thought it was generally felt to be that these days.

This totally plays into the original discussion of the "what caused plague" topic. As even the 1347-1351 outbreak doubted to be Yersinia pests, even more people doubt the earlier, pre-medieval outbreaks to origin with this particular bacteria. Since most historic writers called everything plague that killed people, and most healers from that period being very bad (in modern terms) in describing the symptoms, it's still uncertain.

Seeing that this method worked with 650 year old bones, and we know gene sequencing worked with way older bones, i.e. the neanderthal, we might find out some day. All we need are some bones from that era, which might proof way harder than the 14th century gravesides.

I'm just thankful we are past the age of reason. Few are left who think prayer will heal the plague. If such an epidemic spreads again then we have the help of a better scientific process to curtail it's effect.

Always pleasant to read a story which is essentially "Yup, this bacteria that took out between 1/5th and 1/3rd of the planet's human population is not only still around but has demonstrated an ability to ramp up its lethality by unknown means in response to unknown factors.".

Leaves you hoping it doesn't find an additional vector.

IDK why but the idea to do a little bio engineering and then send blankets to our Chinese friends immediately came to my mind.

How about that? Scientist makes new discovery, has to revise a past assumption. No problem, in fact a pleasant surprise.

So will we hear from all the religious nutjobs denouncing the findings and either saying the Black Plague didn't happen, or that The Devil™ is messing with the results and really it was wicked people who God™ smote?

If you are going put out troll-bait, don't be so overt about it. You end up appearing eerily similar to those whom you denounce.

I'm just thankful we are past the age of reason. Few are left who think prayer will heal the plague. If such an epidemic spreads again then we have the help of a better scientific process to curtail it's effect.

Have you not been reading US political campaign news lately?

Or did I miss some rather subtle humor on your part?

While religion plays a major role in our politics, particularly in the social sphere, people actually forsaking modern medicine entirely in favor of prayer (as opposed to pursuing prayer and going to, you know, a doctor) are a pretty small minority.

Many who turn their back on modern medicine now don't even do it for religious reasons...they do it out of misguided logic (anti-vaxxers, for instance).

Yes, fundies are all around us. But that has little or nothing to do with a potential plague. Grind your axe elsewhere.

Many who turn their back on modern medicine now don't even do it for religious reasons...they do it out of misguided logic (anti-vaxxers, for instance).

Yes, fundies are all around us. But that has little or nothing to do with a potential plague. Grind your axe elsewhere.

Agreed. There is so much antipathy, but religion has little affect on scientific research and perception anymore. Creationism vs Darwinism gets far too much press and attention. The much bigger threat is the self-serving anti-research of special interest groups backed by large corporations. There is a real, tangible effect that this funded 'research' has had on the public perception of climate change and policy towards it.

News Corp. is happy to report on academics arguing about Creationism or attacking religion because it takes the debate away from more worthwhile issues that affect it's supporters (i.e. energy companies, right-wing politicians funded by polluting corporations, et al.).

Many who turn their back on modern medicine now don't even do it for religious reasons...they do it out of misguided logic (anti-vaxxers, for instance).

Yes, fundies are all around us. But that has little or nothing to do with a potential plague. Grind your axe elsewhere.

Agreed. There is so much antipathy, but religion has little affect on scientific research and perception anymore. Creationism vs Darwinism gets far too much press and attention. The much bigger threat is the self-serving anti-research of special interest groups backed by large corporations. There is a real, tangible effect that this funded 'research' has had on the public perception of climate change and policy towards it.

News Corp. is happy to report on academics arguing about Creationism or attacking religion because it takes the debate away from more worthwhile issues that affect it's supporters (i.e. energy companies, right-wing politicians funded by polluting corporations, et al.).

Pharma corps are doing lots of research without the need for public scrutiny, mainly on hair loss and erectile dysfunction.

How about that? Scientist makes new discovery, has to revise a past assumption. No problem, in fact a pleasant surprise.

So will we hear from all the religious nutjobs denouncing the findings and either saying the Black Plague didn't happen, or that The Devil™ is messing with the results and really it was wicked people who God™ smote?

WTF???? This makes no sense. I guess it does to someone whose axe to grind is so great it warps perception. Who has said any of those things about the Black Plague?

Nice to see science still has the ability to admit its wrong about a past event theory and move on to what the new evidence shows us.

I'm also glad to see some scientist looked into the vague story of what happened to the Black Death. I would vote to keep an eye on a strain of germs that wipe out a good portion of the World population.

Are we entirely discounting the outbreak of 541 CE as bubonic plague? I thought it was generally felt to be that these days.

This totally plays into the original discussion of the "what caused plague" topic. As even the 1347-1351 outbreak doubted to be Yersinia pests, even more people doubt the earlier, pre-medieval outbreaks to origin with this particular bacteria. Since most historic writers called everything plague that killed people, and most healers from that period being very bad (in modern terms) in describing the symptoms, it's still uncertain.Seeing that this method worked with 650 year old bones, and we know gene sequencing worked with way older bones, i.e. the neanderthal, we might find out some day. All we need are some bones from that era, which might proof way harder than the 14th century gravesides.

In science it often happens that scientists say, "You know that's a really good argument; my position is mistaken," and then they would actually change their minds and you never hear that old view from them again. They really do it. It doesn't happen as often as it should, because scientists are human and change is sometimes painful. But it happens every day. I cannot recall the last time something like that happened in politics or religion.-Carl Sagan, keynote address at CSICOP conference (1987)

Always pleasant to read a story which is essentially "Yup, this bacteria that took out between 1/5th and 1/3rd of the planet's human population is not only still around but has demonstrated an ability to ramp up its lethality by unknown means in response to unknown factors.".

Leaves you hoping it doesn't find an additional vector.

IDK why but the idea to do a little bio engineering and then send blankets to our Chinese friends immediately came to my mind.

There has been discussion in the medical literature re: high mortality of hosts not being an evolutionary advantage for pathogens. If this is the case and v. pestis did pick up DNA that allowed it to exploit human hosts (to their extreme detriment) it's possible that evolutionary pressure decreased the mortality over time.

Exactly. People look at it's mutation as a good thing for it, b/c they equate power and being able to wipe others out as a good thing. No, it wasn't. Sure, it was good that it was able to wipe out other bacteria to keep them from competing. But it was so detrimental to humans it would wipe out its hosts, too. A really good parasite, virus, bacteria, etc, likes to keep its host alive for continual production. Eventually, over time, it may adapt into a symbiotic relationship, like our digestive bacteria. But this one...it got a circuit crossed and went ballistic without enough control for it to be evolutionary advantageous to itself. It's like saying a wolf evolves into a super wolf that can eat 10 sheep at once...but in doing so it wipes out its entire food source and then dies off. This bacteria had a terminal flaw in its mutation. Fortunately, humans adapted / acclimated to it. And, yes, certain humans in certain parts of the world develop resistances to certain things and vulnerabilities to others they've never been exposed to. So, it was also thought that the black plague may have been an import coming from across the seas; something new from a foreign land that the locals had never been exposed to. It's interesting to see scientists re-explore this to shed light on it.

Always pleasant to read a story which is essentially "Yup, this bacteria that took out between 1/5th and 1/3rd of the planet's human population is not only still around but has demonstrated an ability to ramp up its lethality by unknown means in response to unknown factors.".

Leaves you hoping it doesn't find an additional vector.

IDK why but the idea to do a little bio engineering and then send blankets to our Chinese friends immediately came to my mind.

You don't want to have a lethal/terminal pathogen in you. Maybe it's not the shittiest way to go, but it is among the top 5. Having your body covered in boils, your blood clotting or not clotting, slowly drowning on your own phlegm, your body's immune system destroying itself, losing motor control and capability. It's degrading, it's debilitating, and dehumanizing. If you want to kill someone, just kill them. But using biologicals is a sadistic way to do it, and I would not want to live in a country that thinks it's a good idea to go spreading the plague onto others. That is a huge ethical step in the wrong direction.

So will we hear from all the religious nutjobs denouncing the findings and either saying the Black Plague didn't happen, or that The Devil™ is messing with the results and really it was wicked people who God™ smote?

What in the world are you on about? I've never heard any religious stance on the topic of the Black Plague other than "it was a really bad disease."

Are you confused b/c the illustration attached to the article is credited as coming from the Bible? It may have been included in some edition of the Bible but the events of the New Testament conclude 1300 years before the Black Plague, so there's no deep connection there. (Other than the fact that church was a much more prominent institution in the Middle Ages.)

Edit: I see you've already been sufficiently dogpiled. Well, you asked for it.

Rather than Y. Pestis adapting into something less lethal in was more killing off the humans most susceptible to the Pest.

"Survival of the Sickest" is a good read which explores how many modern ailments arise from adaptations to resist older and more deadly diseases like the Plague. The specific ailment related to the plague is haemochromatosis where the body has an iron overload but it was advantageous against the old plague because it isolated the Pest. Interestingly Ars reported recently that a researcher died from the modern Y. pestis because of this same condition.

Another excellent read about the history and origin of the Plague is "The Great Mortality"

So will we hear from all the religious nutjobs denouncing the findings and either saying the Black Plague didn't happen, or that The Devil™ is messing with the results and really it was wicked people who God™ smote?

What in the world are you on about? I've never heard any religious stance on the topic of the Black Plague other than "it was a really bad disease."

Are you confused b/c the illustration attached to the article is credited as coming from the Bible? It may have been included in some edition of the Bible but the events of the New Testament conclude 1300 years before the Black Plague, so there's no deep connection there. (Other than the fact that church was a much more prominent institution in the Middle Ages.)

Edit: I see you've already been sufficiently dogpiled. Well, you asked for it.

Dogpiled wrongly.

He was making a reference to claims made contemporaneously with the plagues. Claims that the plagues represented the wrath of god on a wicked society were exceptionally common at the time.

John Timmer wrote:For some of the parties involved, this is a bit of an about-face, one that was handled with a degree of candor that's rare in scientific publications. (Citation needed)

T,FTFY.

Quote:

LucidCG wrote:Agreed. There is so much antipathy, but religion has little affect on scientific research and perception anymore. Creationism vs Darwinism gets far too much press and attention. The much bigger threat is the self-serving anti-research of special interest groups backed by large corporations. There is a real, tangible effect that this funded 'research' has had on the public perception of climate change and policy towards it. (Merchants of Doubt by Naomi Orestes and Erik Conway, Bloomsbury Press 2010).

In science it often happens that scientists say, "You know that's a really good argument; my position is mistaken," and then they would actually change their minds and you never hear that old view from them again. They really do it. It doesn't happen as often as it should, because scientists are human and change is sometimes painful. But it happens every day. I cannot recall the last time something like that happened in politics or religion.-Carl Sagan, keynote address at CSICOP conference (1987)

Which is funny, because it happens in science and religion ALL THE TIME. It is among other things how the Mormons still exist and how the republicans and democrats in the US managed to completely switch ideologies several times.

Reading this article brings to mind the dreaded E. Coli. Every time I read about its dangers, I am reminded that it is the same organism I used to buy by the bottle to feed my slime molds. It has been one of the most common laboratory organisms in some part because it was thought to be particularly safe to use. I wonder if the difference in that makes some wild strains so dangerous has been figured out.

Reading this article brings to mind the dreaded E. Coli. Every time I read about its dangers, I am reminded that it is the same organism I used to buy by the bottle to feed my slime molds. It has been one of the most common laboratory organisms in some part because it was thought to be particularly safe to use. I wonder if the difference in that makes some wild strains so dangerous has been figured out.

You do realize that you have E. Coli in your organism right now. Right?

How about that? Scientist makes new discovery, has to revise a past assumption. No problem, in fact a pleasant surprise.

So will we hear from all the religious nutjobs denouncing the findings and either saying the Black Plague didn't happen, or that The Devil™ is messing with the results and really it was wicked people who God™ smote?

People don't have to believe "God smites" the wicked with illness (an assumption that religion was fighting at least 3000 years ago, by the way) to be critics of science. It's childish of science fans like you to say "my way or the highway" -- why not be critical of science as well as everything else? That would only be reasonable.

(And, for the record, I myself am not very impressed with this magical "Science is always right because it's always wrong!" as per the first paragraph of your comment. Neither am I Christian.)

In science it often happens that scientists say, "You know that's a really good argument; my position is mistaken," and then they would actually change their minds and you never hear that old view from them again. They really do it. It doesn't happen as often as it should, because scientists are human and change is sometimes painful. But it happens every day. I cannot recall the last time something like that happened in politics or religion.-Carl Sagan, keynote address at CSICOP conference (1987)

I liked the quote until the last line. While not as prevalent as its occurence in science, it is hardly rare for theologians to change their minds when faced with persuasive counter-argument.

Reading this article brings to mind the dreaded E. Coli. ... I wonder if the difference in that makes some wild strains so dangerous has been figured out.

By and large, yes. It's usually the result of the bacterium producing i.e. enterohemorrhagic toxins due to horizontal gene transfer from prophage infection (a type of virus that integrates directly into the bacterial 'chromosome') or the presence of a (naturally occurring) plasmid within the cell cytoplasm. Bacteria tend to be promiscuous when it comes to taking up DNA from the environment.